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<a href="#pub-methods">Public Member Functions</a>  </div>
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<div class="title">Charmm Class Reference</div>  </div>
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<p><a href="classCharmm-members.html">List of all members.</a></p>
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<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a117a30a5b04bd0e23dc928fc810a97cf"></a><!-- doxytag: member="Charmm::constructor" ref="a117a30a5b04bd0e23dc928fc810a97cf" args="?conf?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>constructor</b> ?conf?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a21b0cfe35ff6e039068346a3e38fae49"></a><!-- doxytag: member="Charmm::start" ref="a21b0cfe35ff6e039068346a3e38fae49" args="?config?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>start</b> ?config?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a59f8d57b7b97e84c3ec1d17b9fe5d769"></a><!-- doxytag: member="Charmm::sendCmd" ref="a59f8d57b7b97e84c3ec1d17b9fe5d769" args="cmd" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>sendCmd</b> cmd</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a9a439e1cb07b033fd702d33cab2a8aac"></a><!-- doxytag: member="Charmm::do" ref="a9a439e1cb07b033fd702d33cab2a8aac" args="cmds?until??condition?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>do</b> cmds?until??condition?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a31a89037ecdc62b92776d89a0d9f378a"></a><!-- doxytag: member="Charmm::abort" ref="a31a89037ecdc62b92776d89a0d9f378a" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>abort</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3b94c792835ac1998925388f49630cdd"></a><!-- doxytag: member="Charmm::setup" ref="a3b94c792835ac1998925388f49630cdd" args="config" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>setup</b> config</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a112fa9f5c922f6b950d8d982b1d8ac44"></a><!-- doxytag: member="Charmm::autosetup" ref="a112fa9f5c922f6b950d8d982b1d8ac44" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>autosetup</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a612ebbfd4873555f2035107fbe423ded"></a><!-- doxytag: member="Charmm::printConfig" ref="a612ebbfd4873555f2035107fbe423ded" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>printConfig</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6bd7757d30b569b5e87222d45d8600e4"></a><!-- doxytag: member="Charmm::genIC" ref="a6bd7757d30b569b5e87222d45d8600e4" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>genIC</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a9a13af20df04d01480acd6bfd0d72acc"></a><!-- doxytag: member="Charmm::refillIC" ref="a9a13af20df04d01480acd6bfd0d72acc" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>refillIC</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ace99d4aada436fc85cf3135aaf0a7a54"></a><!-- doxytag: member="Charmm::getIC" ref="ace99d4aada436fc85cf3135aaf0a7a54" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>getIC</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ac0c9444613ba648f2a9b471379857a4c"></a><!-- doxytag: member="Charmm::getEnergy" ref="ac0c9444613ba648f2a9b471379857a4c" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>getEnergy</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="afec028879009479294264a3ce9ab6fb5"></a><!-- doxytag: member="Charmm::minimize" ref="afec028879009479294264a3ce9ab6fb5" args="type nstep" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>minimize</b> type nstep</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a90ab36107aa00cda3369bcefbccaf2c5"></a><!-- doxytag: member="Charmm::turnon" ref="a90ab36107aa00cda3369bcefbccaf2c5" args="module args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>turnon</b> module args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ae729b15191f7c86c5f8dd14daef1c4a4"></a><!-- doxytag: member="Charmm::turnoff" ref="ae729b15191f7c86c5f8dd14daef1c4a4" args="module" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>turnoff</b> module</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3c5805f2b89fa7e6bec9d038e9ea56de"></a><!-- doxytag: member="Charmm::move" ref="a3c5805f2b89fa7e6bec9d038e9ea56de" args="object args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>move</b> object args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a047a833f6706b6cc1154a62eaa4df146"></a><!-- doxytag: member="Charmm::move2" ref="a047a833f6706b6cc1154a62eaa4df146" args="object args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>move2</b> object args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a46c2c6f2c122341f0abecfb43bca775e"></a><!-- doxytag: member="Charmm::align" ref="a46c2c6f2c122341f0abecfb43bca775e" args="object args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>align</b> object args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3e50a6682431941d38b6647e98d453b7"></a><!-- doxytag: member="Charmm::tilt" ref="a3e50a6682431941d38b6647e98d453b7" args="object args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>tilt</b> object args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6d021e0f4c3d907f7f1af98117122cd9"></a><!-- doxytag: member="Charmm::rotate2" ref="a6d021e0f4c3d907f7f1af98117122cd9" args="object args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>rotate2</b> object args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a875d70d859224d8d08ae7a669883adfe"></a><!-- doxytag: member="Charmm::rotate" ref="a875d70d859224d8d08ae7a669883adfe" args="object args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>rotate</b> object args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3bb6a424f25353b753cc72b6ee8ce793"></a><!-- doxytag: member="Charmm::getCOM" ref="a3bb6a424f25353b753cc72b6ee8ce793" args="object" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>getCOM</b> object</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a29e52529deb77a08f92dda07b1cd4cd7"></a><!-- doxytag: member="Charmm::getOrientation" ref="a29e52529deb77a08f92dda07b1cd4cd7" args="object" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>getOrientation</b> object</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a783f3b2734d186aff2a9619e88636bcb"></a><!-- doxytag: member="Charmm::selectSegs" ref="a783f3b2734d186aff2a9619e88636bcb" args="segments" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>selectSegs</b> segments</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a2b46b343750f7e9097d194b439f9bb50"></a><!-- doxytag: member="Charmm::getReplacable" ref="a2b46b343750f7e9097d194b439f9bb50" args="args" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>getReplacable</b> args</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="af14591e93cac0f62b317605d794d5067"></a><!-- doxytag: member="Charmm::search" ref="af14591e93cac0f62b317605d794d5067" args="fname" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>search</b> fname</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="acd6d759656ff972b0a362f59f73f8bd1"></a><!-- doxytag: member="Charmm::load" ref="acd6d759656ff972b0a362f59f73f8bd1" args="type fname" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>load</b> type fname</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a59d83144833bf97dd3541eff035ad94e"></a><!-- doxytag: member="Charmm::addseg" ref="a59d83144833bf97dd3541eff035ad94e" args="segid seq" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>addseg</b> segid seq</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a89480e4e8c46045350f163802d6193c2"></a><!-- doxytag: member="Charmm::build2ndStruct" ref="a89480e4e8c46045350f163802d6193c2" args="segid?type??start??end?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>build2ndStruct</b> segid?type??start??end?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a71efa5014df03cb9e2dde4cb6fc5a25b"></a><!-- doxytag: member="Charmm::querylength" ref="a71efa5014df03cb9e2dde4cb6fc5a25b" args="segid" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>querylength</b> segid</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a03e1c86b1cabf415e13302172e994c1f"></a><!-- doxytag: member="Charmm::run" ref="a03e1c86b1cabf415e13302172e994c1f" args="setup?configuration?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>run</b> setup?configuration?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3e116a7cb52bf3bd101fd473e4d343cd"></a><!-- doxytag: member="Charmm::complete" ref="a3e116a7cb52bf3bd101fd473e4d343cd" args="setup?configuration?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>complete</b> setup?configuration?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aec97d9b7b04a546306a024446223127f"></a><!-- doxytag: member="Charmm::continue" ref="aec97d9b7b04a546306a024446223127f" args="setup1 with setup2?configuration?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>continue</b> setup1 with setup2?configuration?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a4cdb90a0bfc675ca5c45a9b0bd9e70bc"></a><!-- doxytag: member="Charmm::redo" ref="a4cdb90a0bfc675ca5c45a9b0bd9e70bc" args="setup?configuration?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>redo</b> setup?configuration?</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a52c0e353aaf9cf3d222a5eb87790133d"></a><!-- doxytag: member="Charmm::getSegments" ref="a52c0e353aaf9cf3d222a5eb87790133d" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>getSegments</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a8002064dad06e7f20d3d38ed57fd8d2a"></a><!-- doxytag: member="Charmm::renameSegment" ref="a8002064dad06e7f20d3d38ed57fd8d2a" args="A B" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>renameSegment</b> A B</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6ef2fecce6d31cff7bc9a4a5281b3d34"></a><!-- doxytag: member="Charmm::generate" ref="a6ef2fecce6d31cff7bc9a4a5281b3d34" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>generate</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a45037b5bafc6bd6125e9f1081e866d11"></a><!-- doxytag: member="Charmm::processPsf" ref="a45037b5bafc6bd6125e9f1081e866d11" args="" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>processPsf</b></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a99ed51fa0b17e883d23c85ddc08b05a2"></a><!-- doxytag: member="Charmm::setSolvent" ref="a99ed51fa0b17e883d23c85ddc08b05a2" args="solvation_model?configuration?" -->
&#160;</td><td class="memItemRight" valign="bottom"><b>setSolvent</b> solvation_model?configuration?</td></tr>
</table>
<hr/>The documentation for this class was generated from the following files:<ul>
<li>core/Charmm.tcl</li>
<li>modules/conf/IC.tcl</li>
<li>modules/energy/energy.tcl</li>
<li>modules/geo/cons.tcl</li>
<li>modules/geo/<a class="el" href="geo_8tcl.html">geo.tcl</a></li>
<li>modules/IO/IO.tcl</li>
<li>modules/IO/manipulation.tcl</li>
<li>modules/MD/MD.tcl</li>
<li>modules/sequence/segment.tcl</li>
<li>modules/solvation/implicit.tcl</li>
</ul>
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